normScore
This is the development version of normScore; to use it, please install the devel version of Bioconductor.
Evaluation and Ranking of Normalization Methods for Proteomics Data
Bioconductor version: Development (3.24)
Provides tools to evaluate and rank normalization methods for omics datasets using a composite score derived from multiple performance metrics. The package is designed to support systematic benchmarking and comparison of normalization strategies across datasets and experimental settings. It also includes utilities for summarizing results and visualizing normalization performance.
Author: Julia García Currás [aut, cre]
, Axencia Galega de Innovación (GAIN), Xunta de Galicia [fnd] (Industrial Doctorate Grant 2022-2026, Ref. 23_IN606D_2022_2707220)
Maintainer: Julia García Currás <julia.gcurras at udc.es>
citation("normScore")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("normScore")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("normScore")| Getting started with normScore | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | MultipleComparison, Normalization, Preprocessing, Proteomics, QualityControl, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL-2 |
| Depends | R (>= 4.6) |
| Imports | stats, ggplot2, ggpubr, boot, MASS, rlang, withr |
| System Requirements | |
| URL | https://github.com/juliagcurras/normScore https://juliagcurras.github.io/normScore/ |
| Bug Reports | https://https://github.com/juliagcurras/normScore/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), limma, NormalyzerDE, SummarizedExperiment, S4Vectors, methods, BiocStyle, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | normScore_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | normScore_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/normScore |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/normScore |
| Bioc Package Browser | https://code.bioconductor.org/browse/normScore/ |
| Package Short Url | https://bioconductor.org/packages/normScore/ |
| Package Downloads Report | Download Stats |